Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors
ABSTRACT: Loss of heterzygosity in TP53 Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma
Project description:Loss of heterzygosity in TP53 Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors Overall design: Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma
Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.
Project description:Colorectal cancer arises in part from the cumulative effects of multiple gene lesions. Recent studies in selected cancer types have revealed significant intra-tumor genetic heterogeneity and highlighted its potential role in disease progression and resistance to therapy. We hypothesized the existence of significant intra-tumor genetic heterogeneity in rectal cancers involving variations in localized somatic mutations and copy number abnormalities. Two or three spatially disparate areas from each of six rectal tumors were dissected and subjected to next-generation whole exome DNA sequencing, Oncoscan SNP arrays, and targeted confirmatory sequencing and analysis. The resulting data were integrated to define subclones using SciClone. Mutant-allele tumor heterogeneity (MATH) scores, mutant allele frequency correlation, and mutation percent concordance were calculated, and Copy number analysis including measurement of correlation between samples was performed. Affymetrix OncoScan V3 arrays were run on all tumor samples. The OncoScan array platform consists of a set of 217k probes designed specifically for profiling tumors. The overall resolution of the assay for detecting copy number change generates data at 50-100kb resolution across a set of 891 cancer genes, and 300-400kb across the rest of the genome. Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (Affymetrix, Santa Clara, California). Quality control statistics as well as integrated OSCHP files were generated by OncoScan Console. The standard Affymetrix reference control file for OncoScan data was used for processing the arrays.
Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.
Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues. Copy number analysis using Affymetrix Oncoscan arrays was performed for 29 primary breast cancers
Project description:With the intent of identify alterations associated with the development of distant metastases in Papillary Thyroid Cancer (PTCs), we design a case-control study and performed genome-wide copy number variation analysis by Affymetrix Oncoscan FFPE Kit on 34 PTCs that developed distant metastases (DM-PTCs), 61 PTCs without distant metastases (CTRL-PTCs), and on 7 tissue from distant metastatic site
Project description:For establishing a live-cell biobank of Malignant Pleural Mesothelioma (MPM) samples, cultures of two MPM patients were compared to the original tumor tissue using Affymetrix OncoScan Microarrays for genome-wide CNV and LOH detection. Overall design: Affymetrix OncoScan FFPE Microarrays were performed according the manufacturer's protocol on DNA extracted from FFPE tissue or primary cell cultures
Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues. Overall design: Copy number analysis using Affymetrix Oncoscan arrays was performed for 3 parts of the tumor
Project description:Oncoscan™ Affymetrix array was performed by Affymetrix using DNA extracted from macrodissected FFPE samples Overall design: Copy number analysis was performed on 30 pure LCIS, 30 invLCIS and paired ILC
Project description:Ovarian metastatic tumors that contain component of signet-ring cells are known as Krukenberg tumors and originate mainly from the stomach (76%), intestines (11%), breast (4%) and other organs(1). KTs chiefly affect premenopausal women. Although a few studies have suggested that patients might benefit from metastasectomy with systemic chemotherapy, optimal treatment options are limited, and the prognosis is poor. Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-Krukenberg tumor tissues and primary gastric cancer tissues.